Multiple sequence alignment - TraesCS2A01G331200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G331200 chr2A 100.000 3251 0 0 1 3251 564217387 564220637 0.000000e+00 6004.0
1 TraesCS2A01G331200 chr2A 92.667 150 11 0 992 1141 755700289 755700140 1.960000e-52 217.0
2 TraesCS2A01G331200 chr2A 83.740 123 20 0 1238 1360 185285016 185285138 2.050000e-22 117.0
3 TraesCS2A01G331200 chr2D 93.895 2195 70 21 444 2625 424016051 424013908 0.000000e+00 3253.0
4 TraesCS2A01G331200 chr2D 84.202 614 67 20 966 1563 624297648 624297049 1.310000e-158 569.0
5 TraesCS2A01G331200 chr2D 86.228 501 45 17 2765 3251 424013910 424013420 3.720000e-144 521.0
6 TraesCS2A01G331200 chr2D 95.848 289 8 2 1 285 630269861 630269573 6.350000e-127 464.0
7 TraesCS2A01G331200 chr2D 95.502 289 9 2 1 285 33934449 33934161 2.960000e-125 459.0
8 TraesCS2A01G331200 chr2D 95.502 289 9 2 1 285 630270926 630270638 2.960000e-125 459.0
9 TraesCS2A01G331200 chr2D 96.078 153 4 2 283 435 424016245 424016095 6.970000e-62 248.0
10 TraesCS2A01G331200 chr2D 83.077 130 22 0 1234 1363 165468252 165468123 5.700000e-23 119.0
11 TraesCS2A01G331200 chr2B 92.667 2141 85 24 283 2376 498311740 498309625 0.000000e+00 3018.0
12 TraesCS2A01G331200 chr2B 85.954 477 40 15 2785 3249 498308131 498307670 4.880000e-133 484.0
13 TraesCS2A01G331200 chr2B 91.011 267 12 7 2363 2625 498308501 498308243 1.860000e-92 350.0
14 TraesCS2A01G331200 chr5B 95.156 289 10 2 1 285 429033057 429032769 1.380000e-123 453.0
15 TraesCS2A01G331200 chr5B 94.464 289 12 2 1 285 432877357 432877069 2.980000e-120 442.0
16 TraesCS2A01G331200 chr5B 80.263 152 27 3 1225 1374 369485723 369485873 9.530000e-21 111.0
17 TraesCS2A01G331200 chr3B 95.139 288 10 2 2 285 201560142 201560429 4.950000e-123 451.0
18 TraesCS2A01G331200 chr5A 94.464 289 12 2 1 285 442271012 442270724 2.980000e-120 442.0
19 TraesCS2A01G331200 chr5A 79.866 149 28 2 1227 1374 414934558 414934411 1.230000e-19 108.0
20 TraesCS2A01G331200 chr3D 95.053 283 10 3 1 280 213392647 213392928 2.980000e-120 442.0
21 TraesCS2A01G331200 chr3D 75.661 189 35 8 3014 3194 278063092 278063277 2.080000e-12 84.2
22 TraesCS2A01G331200 chrUn 94.118 289 13 2 1 285 327662671 327662959 1.380000e-118 436.0
23 TraesCS2A01G331200 chrUn 85.165 364 30 14 1219 1561 232286343 232285983 5.160000e-93 351.0
24 TraesCS2A01G331200 chrUn 91.620 179 12 1 966 1141 232287818 232287640 9.010000e-61 244.0
25 TraesCS2A01G331200 chr7A 85.714 147 18 3 2622 2767 688209804 688209948 5.620000e-33 152.0
26 TraesCS2A01G331200 chr1B 86.466 133 16 2 2636 2767 110617165 110617034 9.400000e-31 145.0
27 TraesCS2A01G331200 chr4B 86.400 125 13 3 1448 1570 413500301 413500423 2.030000e-27 134.0
28 TraesCS2A01G331200 chr4B 76.316 190 33 9 3014 3194 419065448 419065262 1.240000e-14 91.6
29 TraesCS2A01G331200 chr4D 85.366 123 18 0 1448 1570 335349327 335349449 9.470000e-26 128.0
30 TraesCS2A01G331200 chr4D 76.316 190 33 9 3014 3194 148509411 148509597 1.240000e-14 91.6
31 TraesCS2A01G331200 chr4D 75.532 188 37 6 3014 3194 354604636 354604821 2.080000e-12 84.2
32 TraesCS2A01G331200 chr4A 85.950 121 13 3 1451 1569 137523974 137523856 3.410000e-25 126.0
33 TraesCS2A01G331200 chr4A 77.249 189 32 7 3014 3194 358187532 358187347 2.060000e-17 100.0
34 TraesCS2A01G331200 chr3A 93.976 83 5 0 1453 1535 514611935 514611853 3.410000e-25 126.0
35 TraesCS2A01G331200 chr6D 91.954 87 7 0 1453 1539 432709198 432709112 4.400000e-24 122.0
36 TraesCS2A01G331200 chr5D 82.609 115 20 0 1230 1344 319254570 319254684 5.740000e-18 102.0
37 TraesCS2A01G331200 chr1D 79.310 145 24 4 3053 3193 209139044 209139186 2.670000e-16 97.1
38 TraesCS2A01G331200 chr6A 76.630 184 32 8 3014 3189 168616069 168615889 1.240000e-14 91.6
39 TraesCS2A01G331200 chr1A 75.936 187 35 7 3014 3193 433911545 433911362 1.610000e-13 87.9
40 TraesCS2A01G331200 chr7D 76.087 184 32 8 3014 3188 207060392 207060572 5.780000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G331200 chr2A 564217387 564220637 3250 False 6004.000000 6004 100.000000 1 3251 1 chr2A.!!$F2 3250
1 TraesCS2A01G331200 chr2D 424013420 424016245 2825 True 1340.666667 3253 92.067000 283 3251 3 chr2D.!!$R4 2968
2 TraesCS2A01G331200 chr2D 624297049 624297648 599 True 569.000000 569 84.202000 966 1563 1 chr2D.!!$R3 597
3 TraesCS2A01G331200 chr2D 630269573 630270926 1353 True 461.500000 464 95.675000 1 285 2 chr2D.!!$R5 284
4 TraesCS2A01G331200 chr2B 498307670 498311740 4070 True 1284.000000 3018 89.877333 283 3249 3 chr2B.!!$R1 2966
5 TraesCS2A01G331200 chrUn 232285983 232287818 1835 True 297.500000 351 88.392500 966 1561 2 chrUn.!!$R1 595

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
879 1518 0.038526 ACGCCGATCGAAAACTCAGT 60.039 50.0 18.66 1.57 41.67 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2704 5760 0.175073 ATCCGCGGAGTACCTGTTTC 59.825 55.0 33.87 0.0 0.0 2.78 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.507733 TTGGTAACCGACTTAAAGCAATTTA 57.492 32.000 0.00 0.00 0.00 1.40
125 126 5.184711 ACTCAACACAATTGCCACAAAATT 58.815 33.333 5.05 0.00 0.00 1.82
199 743 6.239402 CCTTTTCAAATCTCCAATCCACAACT 60.239 38.462 0.00 0.00 0.00 3.16
221 765 4.903054 TGGTAGATCTATCGGACATACGT 58.097 43.478 5.57 0.00 34.94 3.57
245 789 7.530010 GTGAACACATACTTCACAAGCAATAT 58.470 34.615 6.44 0.00 44.69 1.28
322 910 1.135139 GACAGTAGCATTCTCCGAGCA 59.865 52.381 0.00 0.00 0.00 4.26
408 996 5.129485 ACGATCCATTCACCTCTCAAAGTAT 59.871 40.000 0.00 0.00 0.00 2.12
451 1045 4.358851 GAGTCTCTCTGAATGAATGACCG 58.641 47.826 0.00 0.00 31.64 4.79
453 1047 4.950475 AGTCTCTCTGAATGAATGACCGTA 59.050 41.667 0.00 0.00 31.64 4.02
454 1048 5.067153 AGTCTCTCTGAATGAATGACCGTAG 59.933 44.000 0.00 0.00 31.64 3.51
455 1049 4.046938 TCTCTGAATGAATGACCGTAGC 57.953 45.455 0.00 0.00 0.00 3.58
456 1050 2.791560 CTCTGAATGAATGACCGTAGCG 59.208 50.000 0.00 0.00 0.00 4.26
457 1051 1.258982 CTGAATGAATGACCGTAGCGC 59.741 52.381 0.00 0.00 0.00 5.92
460 1054 1.154205 ATGAATGACCGTAGCGCTGC 61.154 55.000 22.90 19.41 0.00 5.25
461 1055 2.511600 AATGACCGTAGCGCTGCC 60.512 61.111 22.90 9.69 0.00 4.85
462 1056 4.530857 ATGACCGTAGCGCTGCCC 62.531 66.667 22.90 10.13 0.00 5.36
473 1096 1.589716 GCGCTGCCCTTGACTCAAAT 61.590 55.000 0.00 0.00 0.00 2.32
497 1128 3.131755 GGCACGGGTAAGTACAACTCTAT 59.868 47.826 0.00 0.00 0.00 1.98
524 1163 2.029844 GCACTCGGCACAGGACTTC 61.030 63.158 0.00 0.00 43.97 3.01
542 1181 3.181479 ACTTCGCACTGTCAGAAAGTACA 60.181 43.478 6.91 0.00 0.00 2.90
594 1233 1.739338 ATCGACCGGAGTGGAGCATC 61.739 60.000 9.46 0.00 42.00 3.91
595 1234 2.105128 GACCGGAGTGGAGCATCG 59.895 66.667 9.46 0.00 42.00 3.84
596 1235 2.362503 ACCGGAGTGGAGCATCGA 60.363 61.111 9.46 0.00 42.00 3.59
597 1236 2.105128 CCGGAGTGGAGCATCGAC 59.895 66.667 0.00 0.00 44.86 4.20
627 1266 3.694394 GCGAAAACGCGACGGACA 61.694 61.111 15.93 0.00 0.00 4.02
879 1518 0.038526 ACGCCGATCGAAAACTCAGT 60.039 50.000 18.66 1.57 41.67 3.41
885 1524 1.579808 GATCGAAAACTCAGTCGCTCG 59.420 52.381 0.00 0.00 37.19 5.03
886 1525 0.589708 TCGAAAACTCAGTCGCTCGA 59.410 50.000 2.56 2.56 37.19 4.04
895 1534 1.004277 CAGTCGCTCGAACACTCACC 61.004 60.000 0.00 0.00 0.00 4.02
1183 3050 4.141756 TGGTTAAGTGGAAGGAACGTGTTA 60.142 41.667 0.00 0.00 0.00 2.41
1241 3121 4.687215 GTGACAGGGCTGCAGCGA 62.687 66.667 31.19 8.68 43.26 4.93
1310 3190 2.665185 AAGCACGGCGAGTTCACC 60.665 61.111 16.62 0.00 0.00 4.02
1373 3259 1.379044 CAACAGGTGCCCCAGGATC 60.379 63.158 0.00 0.00 0.00 3.36
1393 3285 2.267681 ATCCACGCCGTCTCGTTCTC 62.268 60.000 0.00 0.00 41.21 2.87
1394 3286 2.870161 CACGCCGTCTCGTTCTCG 60.870 66.667 0.00 0.00 41.21 4.04
1395 3287 3.352222 ACGCCGTCTCGTTCTCGT 61.352 61.111 0.00 0.00 40.07 4.18
1403 3299 0.799393 TCTCGTTCTCGTCTGAGCTG 59.201 55.000 0.00 0.00 42.26 4.24
1415 3311 0.751452 CTGAGCTGGCTGCATCTCTA 59.249 55.000 18.84 0.00 45.94 2.43
1432 3333 1.933181 TCTATGCCGTTTTGCTGATCG 59.067 47.619 0.00 0.00 0.00 3.69
2145 4052 3.527641 GACGAGGAGGCGGAAGAT 58.472 61.111 0.00 0.00 35.12 2.40
2196 4103 1.002624 GTCGGGGCTGTTTGGATCA 60.003 57.895 0.00 0.00 0.00 2.92
2205 4112 2.730090 GCTGTTTGGATCAGATTGCGTG 60.730 50.000 0.00 0.00 35.20 5.34
2246 4153 1.129251 GCTGACGAATCACATGTGTGG 59.871 52.381 24.63 10.91 45.65 4.17
2249 4156 1.129251 GACGAATCACATGTGTGGCTG 59.871 52.381 24.63 14.24 45.65 4.85
2397 5450 1.969923 CAGGGAAACTGGAAAATGGCA 59.030 47.619 0.00 0.00 43.70 4.92
2399 5452 3.768757 CAGGGAAACTGGAAAATGGCATA 59.231 43.478 0.00 0.00 43.70 3.14
2401 5454 3.428862 GGGAAACTGGAAAATGGCATACG 60.429 47.826 0.00 0.00 0.00 3.06
2482 5538 2.963599 TTTTTGGGGGTCCTGTCTAC 57.036 50.000 0.00 0.00 0.00 2.59
2483 5539 2.127651 TTTTGGGGGTCCTGTCTACT 57.872 50.000 0.00 0.00 0.00 2.57
2484 5540 1.358152 TTTGGGGGTCCTGTCTACTG 58.642 55.000 0.00 0.00 0.00 2.74
2485 5541 0.192566 TTGGGGGTCCTGTCTACTGT 59.807 55.000 0.00 0.00 0.00 3.55
2598 5654 8.871686 ACCATACAACTTTTCTTGAAATGAAC 57.128 30.769 13.49 0.00 28.89 3.18
2621 5677 6.542852 ACATGACGCACTGTAATTCAAATAC 58.457 36.000 0.00 0.00 0.00 1.89
2625 5681 7.959733 TGACGCACTGTAATTCAAATACTTAG 58.040 34.615 0.00 0.00 0.00 2.18
2626 5682 7.064134 TGACGCACTGTAATTCAAATACTTAGG 59.936 37.037 0.00 0.00 0.00 2.69
2627 5683 6.315393 ACGCACTGTAATTCAAATACTTAGGG 59.685 38.462 0.00 0.00 0.00 3.53
2628 5684 6.495706 GCACTGTAATTCAAATACTTAGGGC 58.504 40.000 0.00 0.00 0.00 5.19
2632 5688 7.888546 ACTGTAATTCAAATACTTAGGGCTTGT 59.111 33.333 0.00 0.00 0.00 3.16
2634 5690 8.736244 TGTAATTCAAATACTTAGGGCTTGTTC 58.264 33.333 0.00 0.00 0.00 3.18
2635 5691 5.873179 TTCAAATACTTAGGGCTTGTTCG 57.127 39.130 0.00 0.00 0.00 3.95
2636 5692 4.258543 TCAAATACTTAGGGCTTGTTCGG 58.741 43.478 0.00 0.00 0.00 4.30
2638 5694 3.821421 ATACTTAGGGCTTGTTCGGAG 57.179 47.619 0.00 0.00 0.00 4.63
2639 5695 1.349067 ACTTAGGGCTTGTTCGGAGT 58.651 50.000 0.00 0.00 0.00 3.85
2640 5696 1.275573 ACTTAGGGCTTGTTCGGAGTC 59.724 52.381 0.00 0.00 0.00 3.36
2643 5699 2.593956 GGGCTTGTTCGGAGTCCCT 61.594 63.158 2.80 0.00 32.66 4.20
2644 5700 1.079057 GGCTTGTTCGGAGTCCCTC 60.079 63.158 2.80 0.00 0.00 4.30
2652 5708 3.839432 GGAGTCCCTCCCGCTTCG 61.839 72.222 0.00 0.00 44.36 3.79
2653 5709 3.069318 GAGTCCCTCCCGCTTCGT 61.069 66.667 0.00 0.00 0.00 3.85
2654 5710 3.358076 GAGTCCCTCCCGCTTCGTG 62.358 68.421 0.00 0.00 0.00 4.35
2656 5712 3.379445 TCCCTCCCGCTTCGTGAC 61.379 66.667 0.00 0.00 0.00 3.67
2657 5713 3.382832 CCCTCCCGCTTCGTGACT 61.383 66.667 0.00 0.00 0.00 3.41
2658 5714 2.182030 CCTCCCGCTTCGTGACTC 59.818 66.667 0.00 0.00 0.00 3.36
2659 5715 2.344203 CCTCCCGCTTCGTGACTCT 61.344 63.158 0.00 0.00 0.00 3.24
2660 5716 1.153939 CTCCCGCTTCGTGACTCTG 60.154 63.158 0.00 0.00 0.00 3.35
2661 5717 1.867919 CTCCCGCTTCGTGACTCTGT 61.868 60.000 0.00 0.00 0.00 3.41
2664 5720 1.009389 CCGCTTCGTGACTCTGTTCC 61.009 60.000 0.00 0.00 0.00 3.62
2665 5721 1.009389 CGCTTCGTGACTCTGTTCCC 61.009 60.000 0.00 0.00 0.00 3.97
2667 5723 0.388649 CTTCGTGACTCTGTTCCCGG 60.389 60.000 0.00 0.00 0.00 5.73
2668 5724 0.824595 TTCGTGACTCTGTTCCCGGA 60.825 55.000 0.73 0.00 0.00 5.14
2670 5726 1.079750 GTGACTCTGTTCCCGGAGC 60.080 63.158 0.73 0.00 46.36 4.70
2671 5727 1.533033 TGACTCTGTTCCCGGAGCA 60.533 57.895 0.73 3.68 46.36 4.26
2672 5728 1.216710 GACTCTGTTCCCGGAGCAG 59.783 63.158 22.08 22.08 46.36 4.24
2673 5729 2.125350 CTCTGTTCCCGGAGCAGC 60.125 66.667 23.01 0.75 40.00 5.25
2674 5730 3.672295 CTCTGTTCCCGGAGCAGCC 62.672 68.421 23.01 0.00 40.00 4.85
2691 5747 2.106332 CGGAGCCGCGGTTTAGAT 59.894 61.111 28.70 5.89 0.00 1.98
2692 5748 1.520787 CGGAGCCGCGGTTTAGATT 60.521 57.895 28.70 3.61 0.00 2.40
2695 5751 2.490991 GGAGCCGCGGTTTAGATTTAT 58.509 47.619 28.70 0.00 0.00 1.40
2697 5753 3.303791 GGAGCCGCGGTTTAGATTTATTG 60.304 47.826 28.70 0.00 0.00 1.90
2698 5754 3.537580 AGCCGCGGTTTAGATTTATTGA 58.462 40.909 28.70 0.00 0.00 2.57
2699 5755 3.560068 AGCCGCGGTTTAGATTTATTGAG 59.440 43.478 28.70 0.00 0.00 3.02
2700 5756 3.848554 GCCGCGGTTTAGATTTATTGAGC 60.849 47.826 28.70 1.08 0.00 4.26
2701 5757 3.531982 CGCGGTTTAGATTTATTGAGCG 58.468 45.455 0.00 0.00 38.00 5.03
2702 5758 3.244345 CGCGGTTTAGATTTATTGAGCGA 59.756 43.478 0.00 0.00 45.60 4.93
2703 5759 4.606232 CGCGGTTTAGATTTATTGAGCGAG 60.606 45.833 0.00 0.00 45.60 5.03
2704 5760 4.318831 GCGGTTTAGATTTATTGAGCGAGG 60.319 45.833 0.00 0.00 0.00 4.63
2705 5761 5.047847 CGGTTTAGATTTATTGAGCGAGGA 58.952 41.667 0.00 0.00 0.00 3.71
2707 5763 6.036735 CGGTTTAGATTTATTGAGCGAGGAAA 59.963 38.462 0.00 0.00 0.00 3.13
2708 5764 7.187480 GGTTTAGATTTATTGAGCGAGGAAAC 58.813 38.462 0.00 0.00 0.00 2.78
2709 5765 7.148306 GGTTTAGATTTATTGAGCGAGGAAACA 60.148 37.037 0.00 0.00 0.00 2.83
2710 5766 7.539712 TTAGATTTATTGAGCGAGGAAACAG 57.460 36.000 0.00 0.00 0.00 3.16
2711 5767 4.878397 AGATTTATTGAGCGAGGAAACAGG 59.122 41.667 0.00 0.00 0.00 4.00
2713 5769 4.811969 TTATTGAGCGAGGAAACAGGTA 57.188 40.909 0.00 0.00 0.00 3.08
2714 5770 2.450609 TTGAGCGAGGAAACAGGTAC 57.549 50.000 0.00 0.00 0.00 3.34
2716 5772 1.544691 TGAGCGAGGAAACAGGTACTC 59.455 52.381 0.00 0.00 34.60 2.59
2717 5773 0.896226 AGCGAGGAAACAGGTACTCC 59.104 55.000 0.00 0.00 34.60 3.85
2718 5774 0.458025 GCGAGGAAACAGGTACTCCG 60.458 60.000 0.00 0.00 34.60 4.63
2719 5775 0.458025 CGAGGAAACAGGTACTCCGC 60.458 60.000 0.00 0.00 34.60 5.54
2723 5779 0.175073 GAAACAGGTACTCCGCGGAT 59.825 55.000 31.19 20.63 34.60 4.18
2724 5780 0.175073 AAACAGGTACTCCGCGGATC 59.825 55.000 31.19 20.90 34.60 3.36
2725 5781 1.673808 AACAGGTACTCCGCGGATCC 61.674 60.000 31.19 28.07 34.60 3.36
2726 5782 1.828660 CAGGTACTCCGCGGATCCT 60.829 63.158 31.19 29.70 34.60 3.24
2727 5783 1.076192 AGGTACTCCGCGGATCCTT 60.076 57.895 31.19 15.72 39.05 3.36
2730 5786 1.076559 TACTCCGCGGATCCTTGGA 60.077 57.895 31.19 10.82 0.00 3.53
2732 5788 1.005630 CTCCGCGGATCCTTGGATC 60.006 63.158 31.19 18.64 0.00 3.36
2734 5790 1.301244 CCGCGGATCCTTGGATCTG 60.301 63.158 24.07 26.20 40.11 2.90
2736 5792 0.598680 CGCGGATCCTTGGATCTGAC 60.599 60.000 31.70 23.23 39.65 3.51
2737 5793 0.598680 GCGGATCCTTGGATCTGACG 60.599 60.000 31.70 23.93 39.65 4.35
2738 5794 0.032678 CGGATCCTTGGATCTGACGG 59.967 60.000 26.35 10.22 39.65 4.79
2739 5795 1.414158 GGATCCTTGGATCTGACGGA 58.586 55.000 23.87 0.00 0.00 4.69
2740 5796 1.342819 GGATCCTTGGATCTGACGGAG 59.657 57.143 23.87 0.00 0.00 4.63
2741 5797 0.755686 ATCCTTGGATCTGACGGAGC 59.244 55.000 0.00 0.00 0.00 4.70
2745 5801 2.833582 GGATCTGACGGAGCCGGA 60.834 66.667 5.05 1.34 40.91 5.14
2746 5802 2.725008 GATCTGACGGAGCCGGAG 59.275 66.667 5.05 8.67 44.69 4.63
2760 5816 3.982829 GGAGGTTTCCCGAACAGC 58.017 61.111 0.00 0.00 40.13 4.40
2761 5817 1.375326 GGAGGTTTCCCGAACAGCT 59.625 57.895 0.00 0.00 40.13 4.24
2762 5818 0.673956 GGAGGTTTCCCGAACAGCTC 60.674 60.000 0.00 8.83 40.13 4.09
2763 5819 0.673956 GAGGTTTCCCGAACAGCTCC 60.674 60.000 0.00 0.00 40.13 4.70
2764 5820 1.128188 AGGTTTCCCGAACAGCTCCT 61.128 55.000 0.00 0.00 40.13 3.69
2765 5821 0.250770 GGTTTCCCGAACAGCTCCTT 60.251 55.000 0.00 0.00 40.13 3.36
2766 5822 1.002773 GGTTTCCCGAACAGCTCCTTA 59.997 52.381 0.00 0.00 40.13 2.69
2767 5823 2.355818 GGTTTCCCGAACAGCTCCTTAT 60.356 50.000 0.00 0.00 40.13 1.73
2768 5824 3.344515 GTTTCCCGAACAGCTCCTTATT 58.655 45.455 0.00 0.00 38.18 1.40
2769 5825 3.713826 TTCCCGAACAGCTCCTTATTT 57.286 42.857 0.00 0.00 0.00 1.40
2770 5826 2.985896 TCCCGAACAGCTCCTTATTTG 58.014 47.619 0.00 0.00 0.00 2.32
2771 5827 2.304761 TCCCGAACAGCTCCTTATTTGT 59.695 45.455 0.00 0.00 0.00 2.83
2772 5828 3.081804 CCCGAACAGCTCCTTATTTGTT 58.918 45.455 0.00 0.00 36.54 2.83
2773 5829 3.119849 CCCGAACAGCTCCTTATTTGTTG 60.120 47.826 0.00 0.00 34.18 3.33
2774 5830 3.119849 CCGAACAGCTCCTTATTTGTTGG 60.120 47.826 0.00 0.00 34.18 3.77
2775 5831 3.502211 CGAACAGCTCCTTATTTGTTGGT 59.498 43.478 0.00 0.00 34.18 3.67
2776 5832 4.693566 CGAACAGCTCCTTATTTGTTGGTA 59.306 41.667 0.00 0.00 34.18 3.25
2777 5833 5.390567 CGAACAGCTCCTTATTTGTTGGTAC 60.391 44.000 0.00 0.00 34.18 3.34
2782 5838 7.029563 CAGCTCCTTATTTGTTGGTACATTTC 58.970 38.462 0.00 0.00 39.30 2.17
2896 5952 8.899771 CATAGAAATAGGATATGAATGCATGCA 58.100 33.333 25.04 25.04 35.94 3.96
2919 5975 7.125113 GCACAAAACAAATGATTGGTAAACAG 58.875 34.615 0.00 0.00 41.01 3.16
2939 5996 4.020128 ACAGGGAGATTGTTAAGACCTGAC 60.020 45.833 14.08 0.00 45.14 3.51
2950 6007 5.929992 TGTTAAGACCTGACGGTTTCTATTG 59.070 40.000 0.00 0.00 45.73 1.90
2963 6020 4.402474 GGTTTCTATTGACTGAATTGGGGG 59.598 45.833 0.00 0.00 0.00 5.40
2964 6021 5.261216 GTTTCTATTGACTGAATTGGGGGA 58.739 41.667 0.00 0.00 0.00 4.81
3005 6064 4.071961 ACATGGAAGTTTGCCTTTTTCC 57.928 40.909 0.00 0.00 39.59 3.13
3024 6084 2.969262 TCCTGGGGAAATTTTGTCAACC 59.031 45.455 0.00 0.00 0.00 3.77
3030 6090 2.362717 GGAAATTTTGTCAACCGGGTGA 59.637 45.455 20.95 20.95 0.00 4.02
3039 6099 2.817258 GTCAACCGGGTGAATGATTCAA 59.183 45.455 27.07 0.00 42.15 2.69
3041 6101 3.505680 TCAACCGGGTGAATGATTCAAAG 59.494 43.478 22.79 4.35 42.15 2.77
3045 6105 3.119495 CCGGGTGAATGATTCAAAGGAAC 60.119 47.826 9.78 0.00 42.15 3.62
3061 6122 8.925161 TCAAAGGAACTAAAAACACAAGAATG 57.075 30.769 0.00 0.00 38.49 2.67
3094 6155 7.734942 ACATGGTCAAATTAAAGTCAAACCAT 58.265 30.769 0.00 0.00 44.82 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 1.801178 GAGTACTGTCCAACAAGCTGC 59.199 52.381 0.00 0.00 0.00 5.25
199 743 4.694037 CACGTATGTCCGATAGATCTACCA 59.306 45.833 4.10 0.00 39.76 3.25
221 765 7.686438 ATATTGCTTGTGAAGTATGTGTTCA 57.314 32.000 0.00 0.00 0.00 3.18
245 789 8.134895 GCGAATCCACTTCCAATTTGATAAATA 58.865 33.333 0.00 0.00 0.00 1.40
258 802 1.521681 CGAGGGCGAATCCACTTCC 60.522 63.158 0.00 0.00 40.82 3.46
259 803 1.521681 CCGAGGGCGAATCCACTTC 60.522 63.158 0.00 0.00 40.82 3.01
423 1011 2.954989 TCATTCAGAGAGACTCCGGATG 59.045 50.000 3.57 1.36 0.00 3.51
427 1015 4.358851 GTCATTCATTCAGAGAGACTCCG 58.641 47.826 0.00 0.00 32.40 4.63
451 1045 1.811679 GAGTCAAGGGCAGCGCTAC 60.812 63.158 10.99 3.45 0.00 3.58
453 1047 2.680974 TTTGAGTCAAGGGCAGCGCT 62.681 55.000 2.64 2.64 0.00 5.92
454 1048 1.589716 ATTTGAGTCAAGGGCAGCGC 61.590 55.000 5.56 0.00 0.00 5.92
455 1049 0.169672 CATTTGAGTCAAGGGCAGCG 59.830 55.000 5.56 0.00 0.00 5.18
456 1050 0.529378 CCATTTGAGTCAAGGGCAGC 59.471 55.000 5.56 0.00 0.00 5.25
457 1051 1.180029 CCCATTTGAGTCAAGGGCAG 58.820 55.000 15.32 3.34 31.81 4.85
460 1054 0.890683 GTGCCCATTTGAGTCAAGGG 59.109 55.000 20.95 20.95 42.55 3.95
461 1055 0.523072 CGTGCCCATTTGAGTCAAGG 59.477 55.000 5.56 5.51 0.00 3.61
462 1056 0.523072 CCGTGCCCATTTGAGTCAAG 59.477 55.000 5.56 0.00 0.00 3.02
473 1096 0.035176 GTTGTACTTACCCGTGCCCA 59.965 55.000 0.00 0.00 0.00 5.36
517 1156 1.040646 TTCTGACAGTGCGAAGTCCT 58.959 50.000 1.59 0.00 33.89 3.85
524 1163 3.579709 AGATGTACTTTCTGACAGTGCG 58.420 45.455 6.72 0.00 29.96 5.34
542 1181 4.194720 GCGTCGACGGGCTGAGAT 62.195 66.667 36.13 0.00 40.23 2.75
576 1215 2.362503 ATGCTCCACTCCGGTCGA 60.363 61.111 0.00 0.00 35.57 4.20
577 1216 2.105128 GATGCTCCACTCCGGTCG 59.895 66.667 0.00 0.00 35.57 4.79
578 1217 2.105128 CGATGCTCCACTCCGGTC 59.895 66.667 0.00 0.00 35.57 4.79
579 1218 2.362503 TCGATGCTCCACTCCGGT 60.363 61.111 0.00 0.00 35.57 5.28
580 1219 2.105128 GTCGATGCTCCACTCCGG 59.895 66.667 0.00 0.00 0.00 5.14
597 1236 4.753877 TTCGCCAGCTCGTCGTCG 62.754 66.667 0.00 0.00 38.55 5.12
598 1237 2.019951 TTTTCGCCAGCTCGTCGTC 61.020 57.895 0.00 0.00 0.00 4.20
599 1238 2.028484 TTTTCGCCAGCTCGTCGT 59.972 55.556 0.00 0.00 0.00 4.34
627 1266 1.893808 CAGTCCAAGCAAGCACGGT 60.894 57.895 0.00 0.00 0.00 4.83
879 1518 2.142357 CTGGGTGAGTGTTCGAGCGA 62.142 60.000 0.00 0.00 0.00 4.93
885 1524 1.604278 GTTCTTGCTGGGTGAGTGTTC 59.396 52.381 0.00 0.00 0.00 3.18
886 1525 1.680338 GTTCTTGCTGGGTGAGTGTT 58.320 50.000 0.00 0.00 0.00 3.32
895 1534 4.748679 GCGCTGCGTTCTTGCTGG 62.749 66.667 24.04 0.00 34.72 4.85
914 1553 2.550101 GGTAGGCCGATACGTCGCT 61.550 63.158 0.00 0.00 46.32 4.93
1183 3050 0.944311 CCAGCGACAACAGCTAACGT 60.944 55.000 0.00 0.00 44.06 3.99
1241 3121 4.845580 CGGCAGCTCTTCCCGCAT 62.846 66.667 0.00 0.00 35.14 4.73
1310 3190 4.838486 GTCTGCTCCTCGGCGTCG 62.838 72.222 1.15 1.15 37.82 5.12
1373 3259 2.126071 AACGAGACGGCGTGGATG 60.126 61.111 21.19 6.96 44.86 3.51
1393 3285 2.125229 ATGCAGCCAGCTCAGACG 60.125 61.111 0.00 0.00 45.94 4.18
1394 3286 1.221293 AGATGCAGCCAGCTCAGAC 59.779 57.895 0.00 0.00 45.94 3.51
1395 3287 3.723245 AGATGCAGCCAGCTCAGA 58.277 55.556 0.00 0.00 45.94 3.27
1415 3311 1.064505 CATCGATCAGCAAAACGGCAT 59.935 47.619 0.00 0.00 35.83 4.40
1896 3803 4.124351 TCGGACATGTCGCCCGAC 62.124 66.667 19.90 13.45 46.17 4.79
2145 4052 1.925455 CTTCCCTCCCTCCTTGCCA 60.925 63.158 0.00 0.00 0.00 4.92
2196 4103 1.078848 GTCCCAGAGCACGCAATCT 60.079 57.895 0.00 0.00 0.00 2.40
2246 4153 1.421485 CTCGCCGTGTGAATTCAGC 59.579 57.895 8.80 7.85 0.00 4.26
2249 4156 1.324736 CTAAGCTCGCCGTGTGAATTC 59.675 52.381 0.00 0.00 0.00 2.17
2598 5654 6.775088 AGTATTTGAATTACAGTGCGTCATG 58.225 36.000 0.00 0.00 0.00 3.07
2621 5677 1.405661 GGACTCCGAACAAGCCCTAAG 60.406 57.143 0.00 0.00 0.00 2.18
2625 5681 2.046217 GGGACTCCGAACAAGCCC 60.046 66.667 0.00 0.00 0.00 5.19
2626 5682 3.069778 AGGGACTCCGAACAAGCC 58.930 61.111 0.00 0.00 38.33 4.35
2638 5694 3.379445 TCACGAAGCGGGAGGGAC 61.379 66.667 0.00 0.00 32.99 4.46
2639 5695 3.379445 GTCACGAAGCGGGAGGGA 61.379 66.667 0.00 0.00 41.01 4.20
2640 5696 3.358076 GAGTCACGAAGCGGGAGGG 62.358 68.421 0.00 0.00 41.01 4.30
2643 5699 1.461091 AACAGAGTCACGAAGCGGGA 61.461 55.000 0.00 0.00 36.75 5.14
2644 5700 1.006102 AACAGAGTCACGAAGCGGG 60.006 57.895 0.00 0.00 0.00 6.13
2647 5703 2.828933 GGGAACAGAGTCACGAAGC 58.171 57.895 0.00 0.00 0.00 3.86
2652 5708 1.079750 GCTCCGGGAACAGAGTCAC 60.080 63.158 0.00 0.00 33.52 3.67
2653 5709 1.533033 TGCTCCGGGAACAGAGTCA 60.533 57.895 0.00 0.00 33.52 3.41
2654 5710 1.216710 CTGCTCCGGGAACAGAGTC 59.783 63.158 20.35 0.00 33.52 3.36
2656 5712 2.125350 GCTGCTCCGGGAACAGAG 60.125 66.667 27.29 6.94 33.10 3.35
2657 5713 3.706373 GGCTGCTCCGGGAACAGA 61.706 66.667 27.29 0.00 33.10 3.41
2674 5730 1.087771 AAATCTAAACCGCGGCTCCG 61.088 55.000 28.58 12.15 43.09 4.63
2675 5731 1.944032 TAAATCTAAACCGCGGCTCC 58.056 50.000 28.58 0.00 0.00 4.70
2676 5732 3.558418 TCAATAAATCTAAACCGCGGCTC 59.442 43.478 28.58 0.00 0.00 4.70
2678 5734 3.848554 GCTCAATAAATCTAAACCGCGGC 60.849 47.826 28.58 0.00 0.00 6.53
2679 5735 3.603857 CGCTCAATAAATCTAAACCGCGG 60.604 47.826 26.86 26.86 34.00 6.46
2680 5736 3.244345 TCGCTCAATAAATCTAAACCGCG 59.756 43.478 0.00 0.00 38.37 6.46
2681 5737 4.318831 CCTCGCTCAATAAATCTAAACCGC 60.319 45.833 0.00 0.00 0.00 5.68
2682 5738 5.047847 TCCTCGCTCAATAAATCTAAACCG 58.952 41.667 0.00 0.00 0.00 4.44
2684 5740 7.748847 TGTTTCCTCGCTCAATAAATCTAAAC 58.251 34.615 0.00 0.00 0.00 2.01
2685 5741 7.065803 CCTGTTTCCTCGCTCAATAAATCTAAA 59.934 37.037 0.00 0.00 0.00 1.85
2691 5747 4.015872 ACCTGTTTCCTCGCTCAATAAA 57.984 40.909 0.00 0.00 0.00 1.40
2692 5748 3.695830 ACCTGTTTCCTCGCTCAATAA 57.304 42.857 0.00 0.00 0.00 1.40
2695 5751 1.968493 AGTACCTGTTTCCTCGCTCAA 59.032 47.619 0.00 0.00 0.00 3.02
2697 5753 1.135053 GGAGTACCTGTTTCCTCGCTC 60.135 57.143 0.00 0.00 0.00 5.03
2698 5754 0.896226 GGAGTACCTGTTTCCTCGCT 59.104 55.000 0.00 0.00 0.00 4.93
2699 5755 0.458025 CGGAGTACCTGTTTCCTCGC 60.458 60.000 0.00 0.00 0.00 5.03
2700 5756 0.458025 GCGGAGTACCTGTTTCCTCG 60.458 60.000 0.00 0.00 0.00 4.63
2701 5757 0.458025 CGCGGAGTACCTGTTTCCTC 60.458 60.000 0.00 0.00 0.00 3.71
2702 5758 1.590147 CGCGGAGTACCTGTTTCCT 59.410 57.895 0.00 0.00 0.00 3.36
2703 5759 1.447314 CCGCGGAGTACCTGTTTCC 60.447 63.158 24.07 0.00 0.00 3.13
2704 5760 0.175073 ATCCGCGGAGTACCTGTTTC 59.825 55.000 33.87 0.00 0.00 2.78
2705 5761 0.175073 GATCCGCGGAGTACCTGTTT 59.825 55.000 33.87 13.42 0.00 2.83
2707 5763 2.125961 GGATCCGCGGAGTACCTGT 61.126 63.158 33.87 15.12 0.00 4.00
2708 5764 1.392710 AAGGATCCGCGGAGTACCTG 61.393 60.000 35.09 9.74 0.00 4.00
2709 5765 1.076192 AAGGATCCGCGGAGTACCT 60.076 57.895 31.73 31.73 0.00 3.08
2710 5766 1.067582 CAAGGATCCGCGGAGTACC 59.932 63.158 33.87 31.08 0.00 3.34
2711 5767 1.067582 CCAAGGATCCGCGGAGTAC 59.932 63.158 33.87 24.05 0.00 2.73
2713 5769 1.749334 GATCCAAGGATCCGCGGAGT 61.749 60.000 33.87 20.92 43.71 3.85
2714 5770 1.005630 GATCCAAGGATCCGCGGAG 60.006 63.158 33.87 18.95 43.71 4.63
2723 5779 1.330655 GGCTCCGTCAGATCCAAGGA 61.331 60.000 0.00 0.00 30.55 3.36
2724 5780 1.144936 GGCTCCGTCAGATCCAAGG 59.855 63.158 0.00 0.00 30.55 3.61
2725 5781 1.227089 CGGCTCCGTCAGATCCAAG 60.227 63.158 0.00 0.00 29.35 3.61
2726 5782 2.721167 CCGGCTCCGTCAGATCCAA 61.721 63.158 7.59 0.00 37.81 3.53
2727 5783 3.147595 CCGGCTCCGTCAGATCCA 61.148 66.667 7.59 0.00 37.81 3.41
2730 5786 2.835431 CCTCCGGCTCCGTCAGAT 60.835 66.667 7.59 0.00 37.81 2.90
2732 5788 2.837371 GAAACCTCCGGCTCCGTCAG 62.837 65.000 7.59 2.91 37.81 3.51
2734 5790 2.125633 GAAACCTCCGGCTCCGTC 60.126 66.667 7.59 0.00 37.81 4.79
2747 5803 2.467566 TAAGGAGCTGTTCGGGAAAC 57.532 50.000 0.00 0.00 38.43 2.78
2748 5804 3.713826 AATAAGGAGCTGTTCGGGAAA 57.286 42.857 0.00 0.00 0.00 3.13
2749 5805 3.244770 ACAAATAAGGAGCTGTTCGGGAA 60.245 43.478 0.00 0.00 0.00 3.97
2750 5806 2.304761 ACAAATAAGGAGCTGTTCGGGA 59.695 45.455 0.00 0.00 0.00 5.14
2751 5807 2.711542 ACAAATAAGGAGCTGTTCGGG 58.288 47.619 0.00 0.00 0.00 5.14
2752 5808 3.119849 CCAACAAATAAGGAGCTGTTCGG 60.120 47.826 0.00 0.00 29.70 4.30
2753 5809 3.502211 ACCAACAAATAAGGAGCTGTTCG 59.498 43.478 0.00 0.00 29.70 3.95
2754 5810 5.472137 TGTACCAACAAATAAGGAGCTGTTC 59.528 40.000 0.00 0.00 30.91 3.18
2755 5811 5.381757 TGTACCAACAAATAAGGAGCTGTT 58.618 37.500 0.00 0.00 30.91 3.16
2756 5812 4.980573 TGTACCAACAAATAAGGAGCTGT 58.019 39.130 0.00 0.00 30.91 4.40
2757 5813 6.515272 AATGTACCAACAAATAAGGAGCTG 57.485 37.500 0.00 0.00 39.58 4.24
2758 5814 6.948309 AGAAATGTACCAACAAATAAGGAGCT 59.052 34.615 0.00 0.00 39.58 4.09
2759 5815 7.158099 AGAAATGTACCAACAAATAAGGAGC 57.842 36.000 0.00 0.00 39.58 4.70
2760 5816 9.981114 AAAAGAAATGTACCAACAAATAAGGAG 57.019 29.630 0.00 0.00 39.58 3.69
2770 5826 9.129209 GCAGATCTTAAAAAGAAATGTACCAAC 57.871 33.333 0.00 0.00 41.63 3.77
2771 5827 9.077885 AGCAGATCTTAAAAAGAAATGTACCAA 57.922 29.630 0.00 0.00 41.63 3.67
2772 5828 8.514594 CAGCAGATCTTAAAAAGAAATGTACCA 58.485 33.333 0.00 0.00 41.63 3.25
2773 5829 7.970614 CCAGCAGATCTTAAAAAGAAATGTACC 59.029 37.037 0.00 0.00 41.63 3.34
2774 5830 7.970614 CCCAGCAGATCTTAAAAAGAAATGTAC 59.029 37.037 0.00 0.00 41.63 2.90
2775 5831 7.362920 GCCCAGCAGATCTTAAAAAGAAATGTA 60.363 37.037 0.00 0.00 41.63 2.29
2776 5832 6.573094 GCCCAGCAGATCTTAAAAAGAAATGT 60.573 38.462 0.00 0.00 41.63 2.71
2777 5833 5.809051 GCCCAGCAGATCTTAAAAAGAAATG 59.191 40.000 0.00 0.00 41.63 2.32
2782 5838 3.119352 GGTGCCCAGCAGATCTTAAAAAG 60.119 47.826 0.00 0.00 40.08 2.27
2787 5843 0.991146 TTGGTGCCCAGCAGATCTTA 59.009 50.000 0.00 0.00 40.08 2.10
2896 5952 6.765512 CCCTGTTTACCAATCATTTGTTTTGT 59.234 34.615 0.00 0.00 0.00 2.83
2919 5975 3.522553 CGTCAGGTCTTAACAATCTCCC 58.477 50.000 0.00 0.00 0.00 4.30
2939 5996 4.096382 CCCCAATTCAGTCAATAGAAACCG 59.904 45.833 0.00 0.00 0.00 4.44
2979 6036 5.357742 AAAGGCAAACTTCCATGTTTTCT 57.642 34.783 0.00 0.00 38.85 2.52
2980 6037 6.435430 AAAAAGGCAAACTTCCATGTTTTC 57.565 33.333 0.00 0.00 38.85 2.29
2984 6041 3.711190 AGGAAAAAGGCAAACTTCCATGT 59.289 39.130 8.91 0.00 39.91 3.21
2987 6044 2.433970 CCAGGAAAAAGGCAAACTTCCA 59.566 45.455 8.91 0.00 39.91 3.53
2992 6051 1.419381 TCCCCAGGAAAAAGGCAAAC 58.581 50.000 0.00 0.00 0.00 2.93
3005 6064 2.288763 CCGGTTGACAAAATTTCCCCAG 60.289 50.000 0.00 0.00 0.00 4.45
3024 6084 3.758554 AGTTCCTTTGAATCATTCACCCG 59.241 43.478 0.00 0.00 39.87 5.28
3030 6090 9.883142 TTGTGTTTTTAGTTCCTTTGAATCATT 57.117 25.926 0.00 0.00 31.98 2.57
3039 6099 7.112452 AGCATTCTTGTGTTTTTAGTTCCTT 57.888 32.000 0.00 0.00 0.00 3.36
3102 6163 9.332502 TGGCGTAATAACATTCTAAACATACAT 57.667 29.630 0.00 0.00 0.00 2.29
3115 6176 5.925509 ACATCCTTAGTGGCGTAATAACAT 58.074 37.500 0.00 0.00 35.26 2.71
3124 6185 3.130516 TGAGACTAACATCCTTAGTGGCG 59.869 47.826 0.00 0.00 35.54 5.69
3226 6361 3.716601 AGAAACATGCAAAGGAAAACGG 58.283 40.909 0.00 0.00 0.00 4.44


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.